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Tree species characterise biodiversity, health, economic potential, and resilience of an ecosystem, for example. Tree species classification based on remote sensing data, however, is known to be a challenging task. In this paper, we study for the first time the feasibility of tree species classification using high-density point clouds collected with an airborne close-range multispectral laser scanning system – a technique that has previously proved to be capable of providing stem curve and volume accurately and rapidly for standing trees. To this end, we carried out laser scanning measurements from a helicopter on 53 forest sample plots, each with a size of 32 m × 32 m. The plots covered approximately 5500 trees in total, including Scots pine (Pinus sylvestris L.), Norway spruce (Picea abies (L.) H.Karst.), and deciduous trees such as Downy birch (Betula pubescens Ehrh.) and Silverbirch (Betula pendula Roth). The multispectral laser scanning system consisted of integrated Riegl VUX-1HA, miniVUX-3UAV, and VQ-840-G scanners (Riegl GmbH, Austria) operating at wavelengths of 1550 nm, 905 nm, and 532 nm, respectively. A new approach, layer-by-layer segmentation, was developed for individual tree detection and segmentation from the dense point cloud data. After individual tree segmentation, 249 features were computed for tree species classification, which was tested with approximately 3000 trees. The features described the point cloud geometry as well as single-channel and multi-channel reflectance metrics. Both feature selection and the tree species classification were conducted using the random forest method. Using the layer-by-layer segmentation algorithm, trees in the dominant and co-dominant categories were found with detection rates of 89.5% and 77.9%, respectively, whereas suppressed trees were detected with a success rate of 15.2%–42.3%, clearly improving upon the standard watershed segmentation. The overall accuracy of the tree species classification was 73.1% when using geometric features from the 1550 nm scanner data and 86.6% when combining the geometric features with reflectance information of the 1550 nm data. The use of multispectral reflectance and geometric features improved the overall classification accuracy up to 90.8%. Classification accuracies were as high as 92.7% and 93.7% for dominant and co-dominant trees, respectively.